Fix github sam2 packaging for PyPI release

Signed-off-by: Sachidanand Alle <[email protected]>

.github/workflows/pythonapp.yml

@@ -128,7 +128,7 @@ jobs:
           rm -r build monailabel*.egg-info
 
           # install from wheel
-          python -m pip install `ls "$tmp_dir"/monailabel*.whl`[all]
+          python -m pip install "$tmp_dir"/monailabel*.whl
           python -c 'import monailabel; monailabel.print_config()' 2>&1 | grep -iv "unknown"
           python -c 'import monailabel; print(monailabel.__file__)'
 

.github/workflows/release.yml

@@ -65,7 +65,7 @@ jobs:
           rm -r build monailabel*.egg-info
 
           # install from wheel
-          python -m pip install `ls "$tmp_dir"/monailabel*.whl`[all]
+          python -m pip install "$tmp_dir"/monailabel*.whl
           python -c 'import monailabel; monailabel.print_config()' 2>&1 | grep -iv "unknown"
           python -c 'import monailabel; print(monailabel.__file__)'
 

Dockerfile

@@ -39,4 +39,4 @@ WORKDIR /opt/monailabel
 RUN apt update -y && apt install -y git curl openslide-tools python3 python-is-python3 python3-pip
 RUN python -m pip install --no-cache-dir pytest torch torchvision torchaudio
 COPY --from=build /opt/monailabel/dist/monailabel* /opt/monailabel/dist/
-RUN python -m pip install --no-cache-dir `ls /opt/monailabel/dist/monailabel*.whl`[all]
+RUN python -m pip install --no-cache-dir /opt/monailabel/dist/monailabel*.whl

README.md

@@ -167,12 +167,6 @@ In addition, you can find a table of the basic supported fields, modalities, vie
 <tr>
 </table>
 
-> [**SAM2**](https://github.com/facebookresearch/sam2/)
->
-> By default, SAM2 is included for all the above Apps only when **_python >= 3.10_**
->  - **sam_2d**: for any organ or tissue and others over a given slice/2D image.
->  - **sam_3d**: to support SAM2 propagation over multiple slices (Radiology/MONAI-Bundle).
-
 # Getting Started with MONAI Label
 ### MONAI Label requires a few steps to get started:
 - Step 1: [Install MONAI Label](#step-1-installation)
@@ -185,7 +179,7 @@ In addition, you can find a table of the basic supported fields, modalities, vie
 
 ### Current Stable Version
 <a href="https://pypi.org/project/monailabel/#history"><img alt="GitHub release (latest SemVer)" src="https://img.shields.io/github/v/release/project-monai/monailabel"></a>
-<pre>pip install -U monailabel[all]</pre>
+<pre>pip install -U monailabel</pre>
 
 MONAI Label supports the following OS with **GPU/CUDA** enabled. For more details instruction, please see the installation guides.
 - [Ubuntu](https://docs.monai.io/projects/label/en/latest/installation.html)
@@ -219,6 +213,19 @@ To install the _**latest features**_ using one of the following options:
   <pre>docker run --gpus all --rm -ti --ipc=host --net=host projectmonai/monailabel:latest bash</pre>
 </details>
 
+### SAM-2
+
+> By default, [**SAM2**](https://github.com/facebookresearch/sam2/) model is included for all the Apps when **_python >= 3.10_**
+>  - **sam_2d**: for any organ or tissue and others over a given slice/2D image.
+>  - **sam_3d**: to support SAM2 propagation over multiple slices (Radiology/MONAI-Bundle).
+
+If you are using `pip install monailabel` by default it uses [SAM-2](https://huggingface.co/facebook/sam2-hiera-large) models.
+<br/>
+To use [SAM-2.1](https://huggingface.co/facebook/sam2.1-hiera-large) use one of following options.
+ - Use monailabel [Docker](https://hub.docker.com/r/projectmonai/monailabel) instead of pip package
+ - Run monailabel in dev mode (git checkout)
+ - If you have installed monailabel via pip then uninstall **_sam2_** package `pip uninstall sam2` and then run `pip install -r requirements.txt` or install latest **SAM-2** from it's [github](https://github.com/facebookresearch/sam2/tree/main?tab=readme-ov-file#installation).
+
 ## Step 2 MONAI Label Sample Applications
 
 <h3>Radiology</h3>

monailabel/config.py

@@ -8,14 +8,18 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import os
+from importlib.util import find_spec
 from typing import Any, Dict, List, Optional
 
 from pydantic import AnyHttpUrl
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
+def is_package_installed(name):
+    return False if find_spec(name) is None else True
+
+
 class Settings(BaseSettings):
     MONAI_LABEL_API_STR: str = ""
     MONAI_LABEL_PROJECT_NAME: str = "MONAILabel"
@@ -98,6 +102,19 @@ class Settings(BaseSettings):
     MONAI_ZOO_REPO: str = "Project-MONAI/model-zoo/hosting_storage_v1"
     MONAI_ZOO_AUTH_TOKEN: str = ""
 
+    # Refer: https://github.com/facebookresearch/sam2?tab=readme-ov-file#model-description
+    # Refer: https://huggingface.co/facebook/sam2-hiera-large
+    MONAI_SAM_MODEL_PT = (
+        "https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt"
+        if is_package_installed("SAM-2")
+        else "https://huggingface.co/facebook/sam2-hiera-large/resolve/main/sam2_hiera_large.pt"
+    )
+    MONAI_SAM_MODEL_CFG = (
+        "https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_l.yaml"
+        if is_package_installed("SAM-2")
+        else "https://huggingface.co/facebook/sam2-hiera-large/resolve/main/sam2_hiera_l.yaml"
+    )
+
     model_config = SettingsConfigDict(
         env_file=".env",
         case_sensitive=True,

monailabel/sam2/infer.py

@@ -116,15 +116,8 @@ def __init__(
             self._config.update(config)
 
         # Download PreTrained Model
-        # https://github.com/facebookresearch/sam2?tab=readme-ov-file#model-description
-        # https://huggingface.co/facebook/sam2-hiera-large
-
-        pt_url = "https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt"
-        conf_url = "https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_l.yaml"
-
-        # pt_url = "https://huggingface.co/facebook/sam2-hiera-large/resolve/main/sam2_hiera_large.pt"
-        # conf_url = "https://huggingface.co/facebook/sam2-hiera-large/resolve/main/sam2_hiera_l.yaml"
-
+        pt_url = settings.MONAI_SAM_MODEL_PT
+        conf_url = settings.MONAI_SAM_MODEL_CFG
         sam_pt = pt_url.split("/")[-1]
         sam_conf = conf_url.split("/")[-1]
 

setup.cfg

@@ -70,11 +70,8 @@ install_requires =
     scikit-learn
     scipy
     google-auth>=2.29.0
-
-[options.extras_require]
-all =
-    SAM-2 @ git+https://github.com/facebookresearch/sam2.git@c2ec8e14a185632b0a5d8b161928ceb50197eddc ; python_version >= '3.10'
-    #sam2>=0.4.1; python_version >= '3.10'
+    sam2>=0.4.1; python_version >= '3.10'
+    #SAM-2 @ git+https://github.com/facebookresearch/sam2.git@c2ec8e14a185632b0a5d8b161928ceb50197eddc ; python_version >= '3.10'
 
 [flake8]
 select = B,C,E,F,N,P,T4,W,B9